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A comparative account of gene expression resources, feature-validations and application-based categorizations : Human
Resources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
GEO - Gene Expression Omnibus
A public genomics data repository that supports MIAME-compliant data submissions. Sequence- and array-based data are accepted. It archives and freely distributes microarray, next-generation sequencing, and other forms of high-throughput data. It provides various web-interfaces and applications to query and download the data in GEO.
Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002 Jan 1;30 (1):207-10. PubMed PMID: 11752295; PubMed Central PMCID: PMC99122.
TiGER - Tissue-specific Gene Expression and Regulation
A database for tissue-specific gene expression and regulation. It contains three types of data: tissue-specific gene expression profiles (based on EST data), combinatorial gene regulations, and cis-regulatory module detections. It has gene view, transcription factor view and tissue view. It also provides the preferential expression site for the queried gene.
Liu X, Yu X, Zack DJ, Zhu H, Qian J. TiGER: a database for tissue-specific gene expression and regulation. BMC Bioinformatics. 2008 Jun 9;9:271. PubMed PMID: 18541026; PubMed Central PMCID: PMC2438328.
A universal catalog of protein information on function, sequence, expression, and many others. It has two sections: "UniProtKB/Swiss-Prot" containing manually-annotated records and "UniProtKB/TrEMBL" with computationally analyzed records awaiting manual annotation.
Bairoch A, Apweiler R. The SWISS-PROT protein sequence data bank and its new supplement TREMBL. Nucleic Acids Res. 1996 Jan 1;24(1):21-5. PubMed PMID: 8594581; PubMed Central PMCID: PMC145613.
A cancer microarray database and web-based data mining platform providing gene expression and DNA copy number data. Oncomine provides differentially expressed genes across multiple experiments for various cancers, drug sensitivity, etc. It provides co-expressed genes for a queried gene. The database also has integrated pathways and Gene Ontology annotations.
Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan AM. ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia. 2004 Jan-Feb;6(1):1-6. PubMed PMID: 15068665; PubMed Central PMCID: PMC1635162.

The Oncomine Research Edition, requires login to access and is free for academic and nonprofit organizations. Oncomine Research Premium Edition is a paid-version and provides extra features such as enrichment of user defined gene signatures, export and share results, upload custom concepts.
A human gene compendium that provides gene related information such as function, pathways, expression and interactions for all known and predicted human genes.
Rebhan M, Chalifa-Caspi V, Prilusky J, Lancet D. GeneCards: integrating information about genes, proteins and diseases. Trends Genet. 1997 Apr;13(4):163. PubMed PMID: 9097728.

"Note as per the resource: ""The service is provided free to academic non-profit institutions. All other users require a Commercial License from XenneX, Inc. Unauthorized usage of this service is in breach of the terms and conditions of this web site, and may cause the user to incur fees for usage""."
A database that provides gene expression at EST level, for various normal and disease tissues, and developmental stages. The level of expression is indicated by transcripts per million (TPM).
Boguski MS, Schuler GD. ESTablishing a human transcript map. Nat Genet. 1995 Aug;10(4):369-71. PubMed PMID: 7670480.
A gene annotation resource with a variety of gene report layout views that allows visualization of information from several external resources in the same window. The gene expression profiles in BioGPS are from gene atlas microarray data. For a given gene, the expression patterns are indicated per probe and platform for every tissue/condition shown. It currently supports eight species including human, mouse and rat.
Wu C, Orozco C, Boyer J, Leglise M, Goodale J, Batalov S, Hodge CL, Haase J, Janes J, Huss JW 3rd, Su AI. BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol. 2009;10(11):R130. Epub 2009 Nov 17. PubMed PMID: 19919682; PubMed Central PMCID: PMC3091323.

great tool
Many extra features such as saving the search results, layouts, is possible only by creating an account in BioGPS. BioGPS is also available as an iPhone application.
HPRD - Human Protein Reference Database
A human protein database that integrates literature curated protein information such as protein-protein interactions, post-translational modifications, enzyme/substrate relationships, disease associations, tissue expression, and sub-cellular localization. It also has 'Human Proteinpedia', a community portal for sharing and integration of human protein data.
Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, Surendranath V, Niranjan V, Muthusamy B, Gandhi TK, Gronborg M, Ibarrola N, Deshpande N, Shanker K, Shivashankar HN, Rashmi BP, Ramya MA, Zhao Z, Chandrika KN, Padma N, Harsha HC, Yatish AJ, Kavitha MP, Menezes M, Choudhury DR, Suresh S, Ghosh N, Saravana R, Chandran S, Krishna S, Joy M, Anand SK, Madavan V, Joseph A, Wong GW, Schiemann WP, Constantinescu SN, Huang L, Khosravi-Far R, Steen H, Tewari M, Ghaffari S, Blobe GC, Dang CV, Garcia JG, Pevsner J, Jensen ON, Roepstorff P, Deshpande KS, Chinnaiyan AM, Hamosh A, Chakravarti A, Pandey A. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res. 2003 Oct;13(10):2363-71. PubMed PMID: 14525934; PubMed Central PMCID: PMC403728.

"Note as per the resource: ""Everything in HPRD is free as long as it is not used for commercial purposes. Commercial entitites will have to pay a fee under a licensing arrangement which will be used to make this database even better"". "
Bgee - a dataBase for Gene Expression Evolution
A database to retrieve and compare gene expression patterns between animal species, currrently covering five, including human and mouse. Bgee maps heterogeneous expression data (currently EST, Affymetrix, and in situ hybridization) on anatomical and developmental ontologies.
Parmentier G, Bastian FB, Robinson-Rechavi M. Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy. Bioinformatics. 2010 Jul 15;26(14):1766-71. Epub 2010 Jun 2. PubMed PMID: 20519284; PubMed Central PMCID: PMC2894521.
HuGEIndex - Human Gene Expression Index
A database with high-density oligonucleotide array data for normal human tissues. It has interactive tools to query and visualize the expression data.
Haverty PM, Weng Z, Best NL, Auerbach KR, Hsiao LL, Jensen RV, Gullans SR. HugeIndex: a database with visualization tools for high-density oligonucleotide array data from normal human tissues. Nucleic Acids Res. 2002 Jan 1;30(1):214-7. PubMed PMID: 11752297; PubMed Central PMCID: PMC99144.
A database that contains curated relevant information with respect to gene mapping and genetic diseases. It has mainly three objects: Gene database, Phenotype database and Reference database. The data on each gene include general information, information on DNA, RNA, expression, localization, proteins and pathology.
Frézal J. Genatlas database, genes and development defects. C R Acad Sci III. 1998 Oct;321(10):805-17. Review. PubMed PMID: 9835018.
A Northern blot database that provides expression values (from a blot) for different tissues calculated utilizing ImageJ. The data can be obtained by searching either full text search or list of available northern blots of a specific tissue.
Schlamp K, Weinmann A, Krupp M, Maass T, Galle P, Teufel A. BlotBase: a northern blot database. Gene. 2008 Dec 31;427(1-2):47-50. Epub 2008 Sep 18. PubMed PMID: 18838116.

Database is open for public data submission.
T2D-Db - An Integrated Data Resource on Type-2 Diabetes
A database of candidate genes associated with type 2 diabetes mellitus. It provides genome wide map display of SNP, Genome Wide Association (GWA) and EST data for the candidate genes. The database also includes expression information from microarray data, pathways, protein-protein interactions and disease associated risk factors or complications. It provides a heat map of microarray expression data of selected genes across multiple experiments in an organism.
Agrawal S, Dimitrova N, Nathan P, Udayakumar K, Lakshmi SS, Sriram S, Manjusha N, Sengupta U. T2D-Db: an integrated platform to study the molecular basis of Type 2 diabetes. BMC Genomics. 2008 Jul 7;9:320. PubMed PMID: 18605991; PubMed Central PMCID: PMC2491641.
GUDMAP - GenitoUrinary Molecular Anatomy Project
A gene expression database for the developing organs of the genito-urinary tract. It covers data from immunohistochemistry, in situ hybridization, whole-mount in situ hybridization, transgenic reports & microarray. Mouse strains generated by GUDMAP consortium and other sources, and urogenital system cell lines funded by external sources can also be obtained from GUDMAP.
McMahon AP, Aronow BJ, Davidson DR, Davies JA, Gaido KW, Grimmond S, Lessard JL, Little MH, Potter SS, Wilder EL, Zhang P; GUDMAP project. GUDMAP: the genitourinary developmental molecular anatomy project. J Am Soc Nephrol. 2008 Apr;19(4):667-71. Epub 2008 Feb 20. PubMed PMID: 18287559.
A repository of tissue distribution profiles that identifies and ranks genes in the spectrum of tissue specificity, based on Expressed Sequence Tags (ESTs) data. The database provides information on tissue specific genes, housekeeping genes and a small number of tissues that can be said to share the gene at a certain specificity level. The database currently has many model plant and animal species.
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RefExA - Reference database for gene Expression Analysis
A database that has microarray gene expression data on normal tissues, cancer tissues and cancer cell lines.
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TiProD - Tissue specific Promoter Database
A database that retrieves promoter sequences according to their tissue-specificity or other functional groupings. TiPROD uses the CGAP (Cancer Genome Anatomy Project) data and calculates tissue-specific gene expression for healthy tissues and assigns these tissue specificity to their corresponding regulatory regions based on EPD, DBTSS, and Ensembl annotation. Gene Ontology terms or ID can also be queried, other than UniGene ID.
Chen X, Wu JM, Hornischer K, Kel A, Wingender E. TiProD: the Tissue-specific Promoter Database. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D104-7. PubMed PMID: 16381824; PubMed Central PMCID: PMC1347475.
A database focused on the genetics and genomics of type 1 diabetes susceptibility (T1D), and provides integrated set of data-sets and tools related to T1D. Currently it includes annotated genomic sequences for suspected T1D susceptibility regions; genetic data; microarray data; functional annotation of genes active in beta cells. It also provides ortholog information, tools for analyzing the data and links to pathways and interactions.
Smink LJ, Helton EM, Healy BC, Cavnor CC, Lam AC, Flamez D, Burren OS, Wang Y, Dolman GE, Burdick DB, Everett VH, Glusman G, Laneri D, Rowen L, Schuilenburg H, Walker NM, Mychaleckyj J, Wicker LS, Eizirik DL, Todd JA, Goodman N. T1DBase, a community web-based resource for type 1 diabetes research. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D544-9. PubMed PMID: 15608258; PubMed Central PMCID: PMC540049.
4DXpress - Expression Database in 4D
A platform to query and compare gene expression data for the developmental stages of the major model animals, including zebrafish, drosophila, medaka and mouse. It contains gene expression data acquired through whole mount in situ hybridization. The database can be queried with anatomy ontology based expression annotations across species. It also provides orthologs for the query gene.
Haudry Y, Berube H, Letunic I, Weeber PD, Gagneur J, Girardot C, Kapushesky M, Arendt D, Bork P, Brazma A, Furlong EE, Wittbrodt J, Henrich T. 4DXpress: a database for cross-species expression pattern comparisons. Nucleic Acids Res. 2008 Jan;36(Database issue):D847-53. Epub 2007 Oct 4. PubMed PMID: 17916571; PubMed Central PMCID: PMC2238840.

"Note as per the resource: ""All data is public and searchable without login. Only data which is in the annotation pipeline is not accessible, but will be released, when annotation is complete""."
A curated database that provides microarray expression data for genes involved in mitosis and meiosis, gamete formation and germ line development across species. It also provides other information such as sample annotations, interactions, genome annotation (from Ensembl) and orthologs.
Primig M, Wiederkehr C, Basavaraj R, Sarrauste de Menthière C, Hermida L, Koch R, Schlecht U, Dickinson HG, Fellous M, Grootegoed JA, Hawley RS, Jégou B, Maro B, Nicolas A, Orr-Weaver T, Schedl T, Villeneuve A, Wolgemuth DJ, Yamamoto M, Zickler D, Lamb N, Esposito RE. GermOnline, a new cross-species community annotation database on germ-line development and gametogenesis. Nat Genet. 2003 Dec;35(4):291-2. PubMed PMID: 14647278.

Database displays only expression data obtained with high-density oligonucleotide microarrays (GeneChips).
A database for co-expressed genes and networks in various species. Four types of co-expression networks can be generated: (i) highly co-expressed genes for every gene, (ii) genes with the same Gene Ontology annotation, (iii) genes expressed in the same tissue and (iv) user-defined gene sets. It also provides a view to compare the co-expression patterns across species to estimate the conservation between the two species. It helps in making gene lists for a particular biological function, and functional estimation of a gene. Currently it covers seven model animals and one plant model.
Obayashi T, Hayashi S, Shibaoka M, Saeki M, Ohta H, Kinoshita K. COXPRESdb: a database of coexpressed gene networks in mammals. Nucleic Acids Res. 2008 Jan;36(Database issue):D77-82. Epub 2007 Oct 11. PubMed PMID: 17932064; PubMed Central PMCID: PMC2238883.
GeneSigDB - Curated Gene Signatures
A database of manually curated gene expression signatures from PubMed articles, for many diseases and tissues.
Culhane AC, Schwarzl T, Sultana R, Picard KC, Picard SC, Lu TH, Franklin KR, French SJ, Papenhausen G, Correll M, Quackenbush J. GeneSigDB--a curated database of gene expression signatures. Nucleic Acids Res. 2010 Jan;38(Database issue):D716-25. Epub 2009 Nov 24. PubMed PMID: 19934259; PubMed Central PMCID: PMC2808880.
A manually curated database of heterogeneous gene expression data based on a consistent gene nomenclature. The data has been compiled from a variety of public sources: (i) published expression data, (ii) information on expression profiling reagents provided by commercial suppliers, (iii) official gene nomenclature databases such as Genew for human and (iv) genome-related public databases such as UniGene, RefSeq, EPD and Swiss-Prot. It also provides various gene expression analysis tools and 'MeSH oriented Data Extraction Tools' and various other data extraction tools.
Praz V, Jagannathan V, Bucher P. CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D542-7. PubMed PMID: 14681477; PubMed Central PMCID: PMC308841.
MGEx-Tdb - Mammalian Gene Expression Testis database
A manually curated testis specific database created by a novel meta-analysis approach. It can be queried with various pathological (e.g., testis cancer, azoospermia) and physiological conditions and also different cell types (e.g., spermatocyte, spermatid) and developmental stages (e.g., embryonic, adult). Each genes' expression status is indicated by a reliability score, derieved based on the consensus across multiple samples and studies. The database also provides basic information on each gene.
Acharya KK, Chandrashekar DS, Chitturi N, Shah H, Malhotra V, Sreelakshmi KS, Deepti H, Bajpai A, Davuluri S, Bora P, Rao L. A novel tissue-specific meta-analysis approach for gene expression predictions, initiated with a mammalian gene expression testis database. BMC Genomics. 2010 Aug 11;11:467. PubMed PMID: 20699007; PubMed Central PMCID: PMC3091663.
A database of functional genomics experiments with MIAME and MINSEQE standards. The data can be queried and downloaded. Gene Expression Atlas contains a subset of curated and re-annotated archive data, which can be queried for individual gene expression under different biological conditions across experiments.
Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Rocca-Serra P, Sansone SA. ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 2003 Jan 1;31(1):68-71. PubMed PMID: 12519949; PubMed Central PMCID: PMC165538.
SMD - Stanford Microarray Database
A database that stores raw and normalized data from microarray experiments, and provides web interfaces for researchers to retrieve, analyze and visualize their data.
Sherlock G, Hernandez-Boussard T, Kasarskis A, Binkley G, Matese JC, Dwight SS, Kaloper M, Weng S, Jin H, Ball CA, Eisen MB, Spellman PT, Brown PO, Botstein D, Cherry JM. The Stanford Microarray Database. Nucleic Acids Res. 2001 Jan 1;29(1):152-5. PubMed PMID: 11125075; PubMed Central PMCID: PMC29818.

"Note as per the resource: ""Access to non-public data is limited to registered Stanford researchers and their collaborators""."
A database and software system for the meta-analysis of microarray data. Users can search, access and visualize co-expression and differential expression results across various data-sets.
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"Note as per the resource: ""Most features of Gemma are open to guests. However, to access some functionality, such as data upload, users will need an account""."
caArray - Array Data Management System
An open-source, web accessible array data management system that guides the annotation and exchange of array data using a federated model of local installations whose results are shareable across the cancer Biomedical Informatics Grid.
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PEPR - Public Expression Profiling Resource
A web-based solution, which permits researchers access to Affymetrix expression profiling database through web browser. It allows researchers to query the expression profiles by a number of experimental variables (e.g., tissue, species, chip type). Users can also export all forms of data associated with any particular profile, including raw data files, processed files and interpretation files.
Chen J, Zhao P, Massaro D, Clerch LB, Almon RR, DuBois DC, Jusko WJ, Hoffman EP. The PEPR GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D578-81. PubMed PMID: 14681485; PubMed Central PMCID: PMC308738.
A public repository for a wide range of gene expression high-throughput experimental data, including microarray-based experiments, SAGE, and mass spectrometry proteomic data. It is aimed at storing MIAME-compliant microarray data.
Ikeo K, Ishi-i J, Tamura T, Gojobori T, Tateno Y. CIBEX: center for information biology gene expression database. C R Biol. 2003 Oct-Nov;326(10-11):1079-82. PubMed PMID: 14744116.
CCDB - Cervical cancer gene DataBase
A manually curated database of experimentally validated cervical cancer genes. The database has genes that are up/down-regulated, methylated, amplified and mutated in different stages of cervical cancer. Each gene has information regarding its sequence, location, architecture, function, chromosomal positions, accession numbers, CDS sizes, gene ontology and homology, and is linked to various other external sources. It also includes information related to miRNAs involved in cervical carcinogenesis.
Agarwal SM, Raghav D, Singh H, Raghava GP. CCDB: a curated database of genes involved in cervix cancer. Nucleic Acids Res. 2011 Jan;39(Database issue):D975-9. Epub 2010 Nov 2. PubMed PMID: 21045064; PubMed Central PMCID: PMC3013652.
EDB - Endometrial Data Base
An endometrium specific database that includes gene expression information from hundreds of publications. The physiological/pathological conditions that are covered by the database include natural cycles, menstrual cycles, endometriosis, endometrial cancer, etc.
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EDR - Endometrium Database Resource
A curated database containing information on genes that are significantly over- or under-expressed in the endometrium. It also includes tools that allow, to compare relative RNA expression from different experimental conditions. In addition to expression, the database provides other information related to each gene (e.g., GEO phase expression graphs, ontology terms, and orthologs).
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MGEx-Udb - Mammalian Gene Expression Uterus database
A manually curated uterus specific database created using a novel meta-analysis approach that provides lists of transcribed and dormant genes for various normal, pathological (e.g., cervical cancer, endometrial cancer, endometriosis) and experimental (e.g., treatment, knockout) conditions. Each gene's expression status is indicated by a reliability score, derived based on the consensus across multiple samples and studies. The database provides basic information on each gene, and also allows performing functional analysis and sequence alignment.
Bajpai AK, Davuluri S, Chandrashekar DS, Ilakya S, Dinakaran M, Acharya KK. MGEx-Udb: A Mammalian Uterus Database for Expression-Based Cataloguing of Genes across Conditions, Including Endometriosis and Cervical Cancer. PLoS One. 2012;7(5):e36776. Epub 2012 May 11. PubMed PMID: 22606288.
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